Carbapenem resistance in community-acquired urinary tract infections caused by Klebsiella pneumoniae and Escherichia coli in Morocco: a multicentre study (January 2022–December 2023)

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Abstract Introduction Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) are leading causes of urinary tract infections (UTIs). In Morocco, carbapenem resistance data are scarce and largely hospital-based. We investigated carbapenem-resistant E. coli and K. pneumoniae isolates from community settings in Morocco. Material and Methods In this prospective multicentre study, we analysed 1296 non-duplicate E. coli and K. pneumoniae isolates recovered from outpatients with community-acquired UTIs (CA-UTIs) across 12 Moroccan cities (January 2022–December 2023). Antimicrobial susceptibility testing was performed following EUCAST guidelines. All phenotypically carbapenem-resistant isolates (n = 54, 13 E. coli, et 41 K. pneumoniae) were subjected to whole-genome sequencing (WGS) using Illumina technology to identify resistance determinants, mobile genetic elements and clonal lineages. Results E. coli predominated [n = 1000, 77.2% (95% CI: 74.8–79.4)] while K. pneumoniae accounted for 22.8% [n = 296 (95% CI: 20.6–25.2)]. Carbapenem resistance rates were significantly higher in K. pneumoniae than in E. coli [ertapenem: 21.1% (95% CI: 16.6–26.4) versus 2.4% (95% CI: 1.6–3.6); imipenem: 15.0% (CI: 11.2–19.6) versus 1.9% (95% CI: 1.2–3.0)]. WGS revealed a high clonal diversity [eight sequence types (ST) in E. coli and 12 in K. pneumonnie]. Carbapenemase-mediated resistance was predominant in K. pneumoniae (notably blaNDM-14, blaNDM-7, blaNDM-5 and blaOXA-48). By contrast, E. coli primarily exhibited efflux and permeability defect mechanisms with sporadic carbapenemase-encoding gene carriage (blaNDM or blaOXA-48). The K. pneumoniae international high-risk clone ST147 producing NDM-14 was dominant (n = 23 isolates), followed by ST307 (n = 4), whereas ST410 was the most frequently identified among E. coli (n = 5). Conclusion Carbapenem-resistant E. coli and K. pneumoniae in community UTIs in Morocco, are driven by multiple clones. These findings underscore the urgent need to expand community-based AMR surveillance beyond hospital settings.

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